Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction

We have determined the crystal structure of the enzyme-product complex of t he hammerhead ribozyme by using a reinforced crystal lattice to trap the co mplex prior to dissociation and by employing X-ray holographic image recons truction, a real-space electron density imaging and refinement procedure. S ubsequent to catalysis, the cleavage site residue (C-17), together with its 2',3'-cyclic phosphate, adopts a conformation close to and approximately p erpendicular to the Watson-Crick base-pairing faces of two highly conserved purines in the ribozyme's catalytic pocket (G-5 and A-6). We observe sever al interactions with functional groups on these residues that have been ide ntified as critical for ribozyme activity by biochemical analyses but whose role has defied explanation in terms of previous structural analyses. Thes e interactions may therefore be relevant to the hammerhead ribozyme reactio n mechanism.